PopGenome: What's the difference between two ways of checking population?
0
0
Entering edit mode
2.4 years ago
James Reeve ▴ 130

I'm trying to set my population in the R package PopGenome using the function set.populations(). When I check they're set, GENOME.class@populations returns the names but GENOME.class@region.data@populations is empty.

What's the difference between GENOME.class@populations & GENOME.class@region.data@populations?

Here's my code:

#Upload data
GENOME.class <- readVCF("file/path/Ts_chr1.vcf.gz", numcols = 60000, tid = "chrI", 
    frompos = 1, topos = 27000000, gffpath = "file/path/Ts_chr1.gff3")
#set populations
GENOME.class <- set.populations(GENOME.class, new.populations = list(c("TsAK1","TsAK2"), c("TsOR1","TsOR2")))

#Check populations
GENOME.class@populations
GENOME.class@region.data@populations
popgenome R • 837 views
ADD COMMENT

Login before adding your answer.

Traffic: 1976 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6